Locus 6061

Sequence ID dm3.chr3L
Location 3,399,781 – 3,399,928
Length 147
Max. P 0.907489
window8344 window8345 window8346

overview

Window 4

Location 3,399,781 – 3,399,879
Length 98
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 74.08
Shannon entropy 0.44661
G+C content 0.56896
Mean single sequence MFE -24.95
Consensus MFE -16.41
Energy contribution -17.47
Covariance contribution 1.06
Combinations/Pair 1.11
Mean z-score -1.54
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.19
SVM RNA-class probability 0.907489
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3399781 98 + 24543557
----CUUUUUGCGAAAACCCGGAUGACCCCGACAG-CCCCGGUCGAUCCGGCGGGUUAUCACCACC--AGCCCCUCGCACACACCACAUAUUGUACAUGUGUAUG
----......((((....((((((((((.......-....)))).)))))).(((((.........--))))).))))(((((..((.....))...)))))... ( -27.90, z-score =  -1.55, R)
>droAna3.scaffold_13337 13249409 88 - 23293914
UUUGAUUUUUGCAAGGCCCAAAGUGACCCCAACGGACCCCGGUCGAGCCGCUGGGUUAUCACUGGCCAAGUUGGAAAUAUGCACCACC-----------------
.........((((.((((...(((((.((((.(((..(......)..))).))))...)))))))))....(....)..)))).....----------------- ( -24.00, z-score =   0.06, R)
>droEre2.scaffold_4784 6089996 85 + 25762168
UUUUUUUUUUGCGAAAACCCGGAUGACCCCGACAG-CCCCGGUCGAUCCGGCGGGUUAUCACCACC--AGCCCCUCGCACACACCACA-----------------
.........(((((....((((((((((.......-....)))).)))))).(((((.........--))))).))))).........----------------- ( -24.70, z-score =  -2.27, R)
>droYak2.chr3L 3947058 82 + 24197627
UUUUUUUUUUGCGAAAACCCGGAUGACCCCGACAG-ACCCGGUCGAUCCGGCGGGUUAUCACCACC--AGUUCCUCGCACACAUA--------------------
.........(((((.(((((((((((((.......-....)))).)))))).((.......))...--.)))..)))))......-------------------- ( -22.30, z-score =  -1.44, R)
>droSec1.super_2 3392586 93 + 7591821
----CUUUUUGCGAAAACCCGGAUGACCCCGACAG-CCCCGGUCGAUCCGGCGGGUUAUCACCACC--AGCCCCUCGCACACACCACAUAC---ACAUGUACA--
----.....(((((....((((((((((.......-....)))).)))))).(((((.........--))))).)))))......((((..---..))))...-- ( -25.30, z-score =  -1.98, R)
>droSim1.chr3L 2935468 93 + 22553184
----CUUUUUGCGAAAACCCGGAUGACCCCGACAG-CCCCGGUCGAUCCGGCGGGUUAUCACCACC--AGCCCCUCGCACACACCACAUAC---AUAUGUACA--
----.....(((((....((((((((((.......-....)))).)))))).(((((.........--))))).)))))......((((..---..))))...-- ( -25.50, z-score =  -2.06, R)
>consensus
____CUUUUUGCGAAAACCCGGAUGACCCCGACAG_CCCCGGUCGAUCCGGCGGGUUAUCACCACC__AGCCCCUCGCACACACCACA_________________
.........(((((...(((((((((((............)))).)))))).)(((....)))...........))))).......................... (-16.41 = -17.47 +   1.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,399,781 – 3,399,879
Length 98
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 74.08
Shannon entropy 0.44661
G+C content 0.56896
Mean single sequence MFE -33.29
Consensus MFE -22.59
Energy contribution -22.85
Covariance contribution 0.26
Combinations/Pair 1.24
Mean z-score -1.22
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.792927
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3399781 98 - 24543557
CAUACACAUGUACAAUAUGUGGUGUGUGCGAGGGGCU--GGUGGUGAUAACCCGCCGGAUCGACCGGGG-CUGUCGGGGUCAUCCGGGUUUUCGCAAAAAG----
(((((((((((...)))))).)))))((((((((.((--((..(((((..((((((((.....))))..-....))))))))))))).)))))))).....---- ( -37.20, z-score =  -1.41, R)
>droAna3.scaffold_13337 13249409 88 + 23293914
-----------------GGUGGUGCAUAUUUCCAACUUGGCCAGUGAUAACCCAGCGGCUCGACCGGGGUCCGUUGGGGUCACUUUGGGCCUUGCAAAAAUCAAA
-----------------(((..((((............((((((((((..(((((((((((.....))).))))))))))))))...)))).))))...)))... ( -35.52, z-score =  -2.11, R)
>droEre2.scaffold_4784 6089996 85 - 25762168
-----------------UGUGGUGUGUGCGAGGGGCU--GGUGGUGAUAACCCGCCGGAUCGACCGGGG-CUGUCGGGGUCAUCCGGGUUUUCGCAAAAAAAAAA
-----------------.........((((((((.((--((..(((((..((((((((.....))))..-....))))))))))))).))))))))......... ( -30.00, z-score =  -0.53, R)
>droYak2.chr3L 3947058 82 - 24197627
--------------------UAUGUGUGCGAGGAACU--GGUGGUGAUAACCCGCCGGAUCGACCGGGU-CUGUCGGGGUCAUCCGGGUUUUCGCAAAAAAAAAA
--------------------......((((((.((((--.(.((((((..((((.((((((.....)))-))).))))))))))).))))))))))......... ( -33.50, z-score =  -2.86, R)
>droSec1.super_2 3392586 93 - 7591821
--UGUACAUGU---GUAUGUGGUGUGUGCGAGGGGCU--GGUGGUGAUAACCCGCCGGAUCGACCGGGG-CUGUCGGGGUCAUCCGGGUUUUCGCAAAAAG----
--.((((....---))))........((((((((.((--((..(((((..((((((((.....))))..-....))))))))))))).)))))))).....---- ( -31.50, z-score =  -0.07, R)
>droSim1.chr3L 2935468 93 - 22553184
--UGUACAUAU---GUAUGUGGUGUGUGCGAGGGGCU--GGUGGUGAUAACCCGCCGGAUCGACCGGGG-CUGUCGGGGUCAUCCGGGUUUUCGCAAAAAG----
--...((((((---.......))))))(((((((.((--((..(((((..((((((((.....))))..-....))))))))))))).)))))))......---- ( -32.00, z-score =  -0.35, R)
>consensus
_________________UGUGGUGUGUGCGAGGGGCU__GGUGGUGAUAACCCGCCGGAUCGACCGGGG_CUGUCGGGGUCAUCCGGGUUUUCGCAAAAAG____
..........................((((((((.((.....((((((..((((.(((.((......)).))).)))))))))).)).))))))))......... (-22.59 = -22.85 +   0.26)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,399,837 – 3,399,928
Length 91
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 73.36
Shannon entropy 0.37203
G+C content 0.49978
Mean single sequence MFE -33.53
Consensus MFE -21.32
Energy contribution -20.66
Covariance contribution -0.66
Combinations/Pair 1.15
Mean z-score -1.39
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.516980
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3399837 91 - 24543557
---GUAUGGAUGUGCCACUAGUGCUAUAUAGUGCUACAUACGUACAUACGCACAUACACAUGUACAAUAUGUGGUGUGUGCGAGGGGCUGGUGG
---...........((((((((.((.....((((.......))))...(((((((((((((((...)))))).))))))))).)).)))))))) ( -35.90, z-score =  -1.48, R)
>droEre2.scaffold_4784 6090056 75 - 25762168
GCAUCAUGGCUGUGCCACUAGUGCUAUGGAGCACUACAUACCUACGUG-------------------UGUGUGGUGUGUGCGAGGGGCUGGUGG
((......))....((((((((.((.((..(((((((((((......)-------------------))))))))))...)).)).)))))))) ( -31.20, z-score =  -1.06, R)
>droSim1.chr3L 2935524 86 - 22553184
---GCAUGGAUGUGCCACUAGUGCUAUAUAGUACUACAUACAUACAUACAUCUGUACAUAUG-----UAUGUGGUGUGUGCGAGGGGCUGGUGG
---((((....))))(((((((.((.((((.(((((((((((((..(((....)))..))))-----)))))))))))))...)).))))))). ( -33.50, z-score =  -1.64, R)
>consensus
___GCAUGGAUGUGCCACUAGUGCUAUAUAGUACUACAUACAUACAUAC_____UACA_AUG_____UAUGUGGUGUGUGCGAGGGGCUGGUGG
..............((((((((.((.....((((((((((...........................))))))))))......)).)))))))) (-21.32 = -20.66 +  -0.66)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:00:36 2011